switch default docker image for version_capture to GAR-hosted image; CI change to micromamba #198
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🛠️ Changes Being Made
Updated
/tasks/task_versioning.wdl
which is used in many of the WDL workflows in PHB. This is a small but impactful change.us-docker.pkg.dev/general-theiagen/ubuntu/ubuntu:jammy-20230816
ubuntu:jammy-20230816
downloaded from dockerhub on 2023-09-28Updated CI:
micromamba
to installminiwdl
,cromwell
,pytest
and other dependencies for CI setup. This was done in attempt to save space on the CI runner hard drive. (it helped a little bit)rm -rf ...
commands to cleanup unnecessary stuff that is pre-installed on the CI runners.tests/config/environment.yml
for more discrete control over the CI environment instead of installing on the fly withconda create ...
🧠 Context and Rationale
Doesn't happen often, but occaisionally we see errors in Terra related to pulling docker images from dockerhub. It is said to be one of the least reliable docker image repo's as per the Broad developers.
This would update nearly all WDL workflows to pull from Theiagen's google artifact registry instead of dockerhub, in an attempt to reduce or eliminate the transient errors in Terra.
📋 Workflow/Task Steps
N/A
Inputs
N/A
Outputs
🧪 Testing
Locally
The WDL task ran successfully with miniwdl:
Terra
TheiaCov_FASTA ran successfully on Terra: https://app.terra.bio/#workspaces/theiagen-validations/curtis-sandbox-theiagen-validations/job_history/1cdd9c35-ba44-4855-9a19-2c928b946dd9
🔬 Quality checks
Pull Request (PR) checklist: